Investigating the role of Copy Number Variants in Specific Language Impairment and identification of new candidate genes

Specific language impairment (SLI) is a complex neurodevelopmental disorder defined as an unexpected failure to develop normal language abilities for no obvious reason. Copy number variants (CNVs) are an important source of variation in the susceptibility to neuropsychiatric disorders. Therefore, a CNV study within SLI families was performed to investigate the role of structural variants in SLI. Among the identified CNVs, we focused on CNVs on chromosome 15q11-q13, recurrently observed in neuropsychiatric conditions, and a homozygous exonic microdeletion in ZNF277. Since this microdeletion falls within the AUTS1 locus, a region linked to autism spectrum disorders (ASD), we investigated a potential role of ZNF277 in SLI and ASD. Frequency data and expression analysis of the ZNF277 microdeletion suggested that this variant may contribute to the risk of language impairments in a complex manner, that is independent of the autism risk previously described in this region. Moreover, we identified an affected individual with a dihydropyrimidine dehydrogenase (DPD) deficiency, caused by compound heterozygosity of two deleterious variants in the gene DPYD. Since DPYD represents a good candidate gene for both SLI and ASD, we investigated its involvement in the susceptibility to these two disorders, focusing on the splicing variant rs3918290, the most common mutation in the DPD deficiency. We observed a higher frequency of rs3918290 in SLI cases (1.2%), compared to controls (~0.6%), while no difference was observed in a large ASD cohort. DPYD mutation screening in 4 SLI and 7 ASD families carrying the splicing variant identified six known missense changes and a novel variant in the promoter region. These data suggest that the combined effect of the mutations identified in affected individuals may lead to an altered DPD activity and that rare variants in DPYD might contribute to a minority of cases, in conjunction with other genetic or non-genetic factors.

Investing for impact. An exploration of impact investments in rural Ghana

This thesis offers an exploration of impact and social investments for agricultural development projects in Sub-Saharan Africa. It does so through the case of SustAgric-Africa (SAA), a social enterprise that aims to lift smallholder farmers out of poverty through the promotion of sustainable farming and operates with capital provided by a variety of investors who are committed to pairing financial returns with social and environmental outcomes. The thesis sets off to answer the following research questions: What is the moral dimension that emerges in finance with the establishment of environmental and social criteria? What kind of arrangements do social and impact investments give origin to? Is it possible to talk about a ‘spirit of the gift’ in such arrangements? What happens when abstract and globalizing ideas around ‘impact’ hit the ground? Drawing from the STS and Actor-Network Theory, I look at the formation engendered by social and impact investments in terms of a socio-technical arrangement, and look at the movements of “objects” between the main actors in terms of circuits. In these processes ideas about ‘value’ and ‘values’ articulate in complex ways in the interplay of gift, debt and credit in the relationships among the three main categories of involved actors: investors, SAA, and the farmers. In the case of SAA, I contend that the ways abstract and globalising ideas about ‘impact’ hit the ground produce uncertain results and contribute to the reproduction of inequalities and unequal wealth distribution and accumulation, deepening ongoing processes of financialization. However, my ethnography also reveals how actors depicted as beneficiaries of impact and social policies and resources, far from being passive recipients of policies and resources, actually question and appropriate them, potentially unsettling the whole arrangement and the moral and ethical claims underpinning it.

Il ruolo della grande distribuzione nello sviluppo locale. Un'indagine sul contesto italiano

Supermarkets and hypermarkets still represent a relatively new retailing format in Italy and in its Southern area in particular, where they were introduced decades later than in other Western countries, such as France and the UK in Europe, and the US in America. Nowadays, these retailers have become large organisations potentially capable of influencing local development from an economic, social and urban perspective. The literature concerned with their effects on the local economy, in particular, has focused on labour markets, price dynamics, inter-type competition, instead the impact on macroeconomic factors such as GDP, value added and investments in specific sectors, as agriculture, industry and services. This study tries to fill this gap by empirically investigating associations between key characteristics of these retailers and specific macroeconomic factors.

Effects of pesticides on honey bees (Apis mellifera L.): study of a specific route of exposure and evaluation of biochemical-physiological changes in the assessment of the pesticides toxicity

In this study, some important aspects of the relationship between honey bees (Apis mellifera L.) and pesticides have been investigated. In the first part of the research, the effects of the exposure of honey bees to neonicotinoids and fipronil contaminated dusts were analyzed. In fact, considerable amounts of these pesticides, employed for maize seed dressing treatments, may be dispersed during the sowing operations, thus representing a way of intoxication for honey bees. In particular, a specific way of exposure to this pesticides formulation, the indirect contact, was taken into account. To this aim, we conducted different experimentations, in laboratory, in semi-field and in open field conditions in order to assess the effects on mortality, foraging behaviour, colony development and capacity of orientation. The real dispersal of contaminated dusts was previously assessed in specific filed trials. In the second part, the impact of various pesticides (chemical and biological) on honey bee biochemical-physiological changes, was evaluated. Different ways and durations of exposure to the tested products were also employed. Three experimentations were performed, combining Bt spores and deltamethrin, Bt spores and fipronil, difenoconazole and deltamethrin. Several important enzymes (GST, ALP, SOD, CAT, G6PDH, GAPDH) were selected in order to test the pesticides induced variations in their activity. In particular, these enzymes are involved in different pathways of detoxification, oxidative stress defence and energetic metabolism. The results showed a significant effect on mortality of neonicotinoids and fipronil contaminated dusts, both in laboratory and in semi-field trials. However, no effects were evidenced in honey bees orientation capacity. The analysis of different biochemical indicators highlighted some interesting physiological variations that can be linked to the pesticide exposure. We therefore stress the attention on the possibility of using such a methodology as a novel toxicity endpoint in environmental risk assessment.

Study of the circulation processes in the northern Adriatic sea - coastal area and Venice lagoon inlets

This work is a detailed study of hydrodynamic processes in a defined area, the littoral in front of the Venice Lagoon and its inlets, which are complex morphological areas of interconnection. A finite element hydrodynamic model of the Venice Lagoon and the Adriatic Sea has been developed in order to study the coastal current patterns and the exchanges at the inlets of the Venice Lagoon. This is the first work in this area that tries to model the interaction dynamics, running together a model for the lagoon and the Adriatic Sea. First the barotropic processes near the inlets of the Venice Lagoon have been studied. Data from more than ten tide gauges displaced in the Adriatic Sea have been used in the calibration of the simulated water levels. To validate the model results, empirical flux data measured by ADCP probes installed inside the inlets of Lido and Malamocco have been used and the exchanges through the three inlets of the Venice Lagoon have been analyzed. The comparison between modelled and measured fluxes at the inlets outlined the efficiency of the model to reproduce both tide and wind induced water exchanges between the sea and the lagoon. As a second step, also small scale processes around the inlets that connect the Venice lagoon with the Northern Adriatic Sea have been investigated by means of 3D simulations. Maps of vorticity have been produced, considering the influence of tidal flows and wind stress in the area. A sensitivity analysis has been carried out to define the importance of the advection and of the baroclinic pressure gradients in the development of vortical processes seen along the littoral close to the inlets. Finally a comparison with real data measurements, surface velocity data from HF Radar near the Venice inlets, has been performed, which allows for a better understanding of the processes and their seasonal dynamics. The results outline the predominance of wind and tidal forcing in the coastal area. Wind forcing acts mainly on the mean coastal current inducing its detachment offshore during Sirocco events and an increase of littoral currents during Bora events. The Bora action is more homogeneous on the whole coastal area whereas the Sirocco strengthens its impact in the South, near Chioggia inlet. Tidal forcing at the inlets is mainly barotropic. The sensitivity analysis shows how advection is the main physical process responsible for the persistent vortical structures present along the littoral between the Venice Lagoon inlets. The comparison with measurements from HF Radar not only permitted a validation the model results, but also a description of different patterns in specific periods of the year. The success of the 2D and the 3D simulations on the reproduction both of the SSE, inside and outside the Venice Lagoon, of the tidal flow, through the lagoon inlets, and of the small scale phenomena, occurring along the littoral, indicates that the finite element approach is the most suitable tool for the investigation of coastal processes. For the first time, as shown by the flux modeling, the physical processes that drive the interaction between the two basins were reproduced.

Morphological transitions in molecular and polymeric materials: patterning, fabrication, devices

This thesis individuates and characterizes irreversible transformations occurring in specific organic and oligomeric/polymeric thin films. These transformations are dewetting in discotic liquid crystals thin films and dewetting and smoothing in oligomeric and polyemeric films. Irreversible transformations are extensively characterized by means of optical and atomic force microscopy. In the case of discotic liquid crystals films the morphological characterization is performed sinchronically with electrical measurements of current during dewetting.

Investigating the role of single point mutations in the human proteome: a computational study

In the post genomic era with the massive production of biological data the understanding of factors affecting protein stability is one of the most important and challenging tasks for highlighting the role of mutations in relation to human maladies. The problem is at the basis of what is referred to as molecular medicine with the underlying idea that pathologies can be detailed at a molecular level. To this purpose scientific efforts focus on characterising mutations that hamper protein functions and by these affect biological processes at the basis of cell physiology. New techniques have been developed with the aim of detailing single nucleotide polymorphisms (SNPs) at large in all the human chromosomes and by this information in specific databases are exponentially increasing. Eventually mutations that can be found at the DNA level, when occurring in transcribed regions may then lead to mutated proteins and this can be a serious medical problem, largely affecting the phenotype. Bioinformatics tools are urgently needed to cope with the flood of genomic data stored in database and in order to analyse the role of SNPs at the protein level. In principle several experimental and theoretical observations are suggesting that protein stability in the solvent-protein space is responsible of the correct protein functioning. Then mutations that are found disease related during DNA analysis are often assumed to perturb protein stability as well. However so far no extensive analysis at the proteome level has investigated whether this is the case. Also computationally methods have been developed to infer whether a mutation is disease related and independently whether it affects protein stability. Therefore whether the perturbation of protein stability is related to what it is routinely referred to as a disease is still a big question mark. In this work we have tried for the first time to explore the relation among mutations at the protein level and their relevance to diseases with a large-scale computational study of the data from different databases. To this aim in the first part of the thesis for each mutation type we have derived two probabilistic indices (for 141 out of 150 possible SNPs): the perturbing index (Pp), which indicates the probability that a given mutation effects protein stability considering all the “in vitro” thermodynamic data available and the disease index (Pd), which indicates the probability of a mutation to be disease related, given all the mutations that have been clinically associated so far. We find with a robust statistics that the two indexes correlate with the exception of all the mutations that are somatic cancer related. By this each mutation of the 150 can be coded by two values that allow a direct comparison with data base information. Furthermore we also implement computational methods that starting from the protein structure is suited to predict the effect of a mutation on protein stability and find that overpasses a set of other predictors performing the same task. The predictor is based on support vector machines and takes as input protein tertiary structures. We show that the predicted data well correlate with the data from the databases. All our efforts therefore add to the SNP annotation process and more importantly found the relationship among protein stability perturbation and the human variome leading to the diseasome.

Aging in human liver and skeletal muscle: studies on proteasomes

Aging is a complex phenomenon that affects organs and tissues at a different rate. With advancing age, the skeletal muscle undergoes a progressive loss of mass and strength, a process known as sarcopenia that leads to a decreased mobility and increased risk of falls and invalidity. On the other side, another organ such as the liver that is endowed with a peculiar regenerative capacity seems to be only marginally affected by aging. Accordingly, clinical data indicate that liver transplantation from aged subjects has, in specific conditions, function and duration comparable to those achievable with grafts of liver from young donors. The molecular mechanisms involved in these peculiar aging patterns are still largely unknown, but it is conceivable that protein degradation machineries might play an important role, as they are responsible for the maintenance of cellular homeostasis. Indeed, it has been suggested that alteration of proteostasis may contribute to the onset and progression of several age-related pathological conditions, including skeletal muscle wasting and sarcopenia, as well as to the aging phenotypes. The ubiquitin-proteasome system (UPS) is one of the most important cellular pathways for intracellular degradation of short-lived as well as damaged proteins. To date, studies on the age-related modifications of proteasomes in liver and skeletal muscle were performed prevalently in rodents, with controversial results, while only preliminary observations have been obtained in human liver and skeletal muscle. In this scenario, we want to investigate and characterize in humans the age-related modifications of proteasomes of these two different organs.

Essays in Industrial Organization and Information Technology

Chapter 1 studies how consumers’ switching costs affect the pricing and profits of firms competing in two-sided markets such as Apple and Google in the smartphone market. When two-sided markets are dynamic – rather than merely static – I show that switching costs lower the first-period price if network externalities are strong, which is in contrast to what has been found in one-sided markets. By contrast, switching costs soften price competition in the initial period if network externalities are weak and consumers are more patient than the platforms. Moreover, an increase in switching costs on one side decreases the first-period price on the other side. Chapter 2 examines firms’ incentives to invest in local and flexible resources when demand is uncertain and correlated. I find that market power of the monopolist providing flexible resources distorts investment incentives, while competition mitigates them. The extent of improvement depends critically on demand correlation and the cost of capacity: under social optimum and monopoly, if the flexible resource is cheap, the relationship between investment and correlation is positive, and if it is costly, the relationship becomes negative; under duopoly, the relationship is positive. The analysis also sheds light on some policy discussions in markets such as cloud computing. Chapter 3 develops a theory of sequential investments in cybersecurity. The regulator can use safety standards and liability rules to increase security. I show that the joint use of an optimal standard and a full liability rule leads to underinvestment ex ante and overinvestment ex post. Instead, switching to a partial liability rule can correct the inefficiencies. This suggests that to improve security, the regulator should encourage not only firms, but also consumers to invest in security.

Better Regulation in Latin American Countries: A tool for accountability?

In the last few years, a steadily increasing number of Latin American countries have been adopting policy assessment instruments and new governance structures for them, as part of their policymaking process. Even though the literature argues that these instruments serve, among other things, as tools for accountability, for this to be so, it is necessary to take into account the legal system, decision-making process, and regulatory relationships that exist in the adopting countries. This Thesis researches the policy assessment arrangements adopted and implemented in the Latin American region to understand why are these countries adopting and implementing tools for policy evaluation? Can this contribute towards regulatory accountability, and if so, in which conditions? The Thesis first analyzes the rationales that these countries might have to adopt these regulatory policy arrangements. It then studies the various tools used for policy assessment, paying attention to the scope of the assessments, the times and the stages on which regulations are assessed, referred to as the Policy Evaluation Cycle (PEC), as well as to the governance of these processes. The Thesis develops a framework where each of these components are organized and classified based on which goals or rationales they serve. This can assist countries on deciding how to implement their policy evaluation arrangements, to serve their own goals. Since all of the studied countries have presidential systems, this Thesis studies how regulations are made in this system, and the multiple needed delegations for policymaking, which results in various regulatory relationships. Thus, the desired accountability of policymakers towards their different forums makes relevant the adoption this agenda for regulatory accountability reasons. Bringing to together the literatures on public law, accountability and policy evaluation, this Thesis builds a framework for assessing the contribution towards accountability that each stage of the PEC might have in a specific regulatory relationship. The framework shows to which degree the stages, and the cycle as a whole, contribute towards accountability in specific relationships of a presidential constitutional system. The results evidence that even when a policy assessment structure might contribute towards accountability, this contribution is not absolute as it only operates in specific regulatory relationships, and even more, only in some stages of the PEC contributing at different degrees. This framework can be used by governments or regulatory agencies as an instrument to assess the contribution to accountability of their existing or potential regulatory policy structures in order to improve it.

Altered transcriptional and epigenetic regulation affects brain cells proliferation and differentiation in the ultra-rare genetic demyelinating disease AGC1 deficiency: a study on in vitro models

AGC1 deficiency is a rare demyelinating disease caused by mutations in the SLC25A12 gene, which encodes for the mitochondrial glutamate-aspartate carrier 1 (AGC1/Alarar), highly expressed in the central nervous system. In neurons, impairment in AGC1 activity leads to reduction in N-acetyl-aspartate, the main lipid precursor for myelin synthesis (Profilo et al., 2017); in oligodendrocytes progenitors cells, AGC1 down regulation has been related to early arrest proliferation and premature differentiation (Petralla et al., 2019). Additionally, in vivo AGC1 deficiency models i.e., heterozygous mice for AGC1 knock-out and neurospheres from their subventricular zone, respectively, showed a global decrease in cells proliferation and a switch in neural stem cells (NSCs) commitment, with specific reduction in OPCs number and increase in neural and astrocytic pools (Petralla et al., 2019). Therefore, the present study aims to investigate the transcriptional and epigenetic regulation underlying the alterations observed in OPCs and NSCs biological mechanisms, in either AGC1 deficiency models of Oli-neu cells (murine immortalized oligodendrocytes precursors cells), partially silenced by a shRNA for SLC25A12 gene, and SVZ-derived neurospheres from AGC1+/- mice. Western blot and immunofluorescence analysis revealed significant variations in the expression of transcription factors involved in brain cells’ proliferation and differentiation, in association with altered histone post-translational modifications, as well as histone acetylases (HATs) and deacetylases (HDACs) activity/expression, suggesting an improper transcriptional and epigenetic regulation affecting both AGC1 deficiency in vitro models. Furthermore, given the large role of acetylation in controlling in specific time-windows OPC maturation (Hernandez and Casaccia; 2015), pharmacological HATs/HDACs inhibitions were performed, confirming the involvement of chromatin remodelling enzymes in the altered proliferation and early differentiation observed in the AGC1 deficiency models of siAGC1 Oli-neu cells and AGC1+/- mice-derived neurospheres.

"Ancestry, gender and language - The role of culture in economic development"

This thesis is a combination of research questions in development economics and economics of culture, with an emphasis on the role of ancestry, gender and language policies in shaping inequality of opportunities and socio-economic outcomes across different segments of a society. The first chapter shows both theoretically and empirically that heterogeneity in risk attitudes can be traced to the ethnic origins and ancestral way of living. In particular, I construct a measure of historical nomadism at the ethnicity level and link it to contemporary individual-level data on various proxies of risk attitudes. I exploit exogenous variation in biodiversity to build a novel instrument for nomadism: distance to domestication points. I find that descendants of ethnic groups that historically practiced nomadism (i) are more willing to take risks, (ii) value security less, and (iii) have riskier health behavior. The second chapter evaluates the nature of a trade-off between the advantages of female labor participation and the positive effects of female education. This work exploits a triple difference identification strategy relying on exogenous spike in cotton price and spatial variation in suitability for cotton, and split sample analyses based on the exogenous allocation of land contracts. Results show that gender differences in parental investments in patriarchal societies can be reinforced by the type of agricultural activity, while positive economic shocks may further exacerbate this bias, additionally crowding out higher possibilities to invest in female education. The third chapter brings novel evidence of the role of the language policy in building national sentiments, affecting educational and occupational choices. Here I focus on the case of Uzbekistan and estimate the effects of exposure to the Latin alphabet on informational literacy, education and career choices. I show that alphabet change affects people's informational literacy and the formation of certain educational and labour market trends.

Genes involved in germline regulative pathways in metazoa: an integrative approach to investigate a key feature of animal biology

In Metazoa, the germline represents the cell lineage devoted to transmission of genetic heredity across generations. Its functions intuitively evoke the crucial roles that it plays in the development of a new organism and in the evolution of the species. Germline establishment is tightly tied to animal multicellularity itself, in which the complex differentiation of cell lineages is favoured by the confinement of totipotency in specific cell populations. In the present thesis, I addressed the subject of germline characterization in animals through different approaches, in an attempt to cover different sides and scales. First, I investigated the extent and nature of shared differentially transcribed molecular factors in 10 different species germline-related lineages. I observed that newly evolved genes are less likely to be involved in germline-related mechanisms and that the mostly shared transcriptional signal across the species considered was the upregulation of genes associated to proper DNA replication, instead of the expected transcriptional and post-transcriptional regulation, that apparently have a higher level of lineage-specificity. I then focused on the evolutionary history of Tudor domain containing proteins, a gene family that underwent germline-associated expansions in animals. Using data from 24 holozoan phyla, I could confirm the previously proposed evolution of the Tudor domain secondary structure. Also, I associated lineage-specific family reductions and expansions to peculiar genomic dynamics and to the evolution of germline-associated piRNA pathway of retrotransposon silencing. Lastly, I characterized and investigated the expression of the Tudor protein TDRD7 in the clam Ruditapes philippinarum. Through immunolocalization, I could compare its expression profiles in gametogenic specimens to the previously characterized germline marker vasa. Combining results with literature, I proposed that, in this species, TDRD7 is involved in the assembly of germ granules, i.e. cytoplasmic structures associated to germline differentiation in virtually all animals, but whose assemblers can be taxon specific.

PCM-based in-memory computing: architectures, circuits and applications

Analog In-memory Computing (AIMC) has been proposed in the context of Beyond Von Neumann architectures as a valid strategy to reduce internal data transfers energy consumption and latency, and to improve compute efficiency. The aim of AIMC is to perform computations within the memory unit, typically leveraging the physical features of memory devices. Among resistive Non-volatile Memories (NVMs), Phase-change Memory (PCM) has become a promising technology due to its intrinsic capability to store multilevel data. Hence, PCM technology is currently investigated to enhance the possibilities and the applications of AIMC. This thesis aims at exploring the potential of new PCM-based architectures as in-memory computational accelerators. In a first step, a preliminar experimental characterization of PCM devices has been carried out in an AIMC perspective. PCM cells non-idealities, such as time-drift, noise, and non-linearity have been studied to develop a dedicated multilevel programming algorithm. Measurement-based simulations have been then employed to evaluate the feasibility of PCM-based operations in the fields of Deep Neural Networks (DNNs) and Structural Health Monitoring (SHM). Moreover, a first testchip has been designed and tested to evaluate the hardware implementation of Multiply-and-Accumulate (MAC) operations employing PCM cells. This prototype experimentally demonstrates the possibility to reach a 95% MAC accuracy with a circuit-level compensation of cells time drift and non-linearity. Finally, empirical circuit behavior models have been included in simulations to assess the use of this technology in specific DNN applications, and to enhance the potentiality of this innovative computation approach.

A ROS-based software architecture for a versatile collaborative dual-armed autonomous mobile robot for the manufacturing industry

The industrial context is changing rapidly due to advancements in technology fueled by the Internet and Information Technology. The fourth industrial revolution counts integration, flexibility, and optimization as its fundamental pillars, and, in this context, Human-Robot Collaboration has become a crucial factor for manufacturing sustainability in Europe. Collaborative robots are appealing to many companies due to their low installation and running costs and high degree of flexibility, making them ideal for reshoring production facilities with a short return on investment. The ROSSINI European project aims to implement a true Human-Robot Collaboration by designing, developing, and demonstrating a modular and scalable platform for integrating human-centred robotic technologies in industrial production environments. The project focuses on safety concerns related to introducing a cobot in a shared working area and aims to lay the groundwork for a new working paradigm at the industrial level. The need for a software architecture suitable to the robotic platform employed in one of three use cases selected to deploy and test the new technology was the main trigger of this Thesis. The chosen application consists of the automatic loading and unloading of raw-material reels to an automatic packaging machine through an Autonomous Mobile Robot composed of an Autonomous Guided Vehicle, two collaborative manipulators, and an eye-on-hand vision system for performing tasks in a partially unstructured environment. The results obtained during the ROSSINI use case development were later used in the SENECA project, which addresses the need for robot-driven automatic cleaning of pharmaceutical bins in a very specific industrial context. The inherent versatility of mobile collaborative robots is evident from their deployment in the two projects with few hardware and software adjustments. The positive impact of Human-Robot Collaboration on diverse production lines is a motivation for future investments in research on this increasingly popular field by the industry.